| Year |
Citation |
Score |
| 2021 |
Khakzad H, Vermeul S, Malmström L. Quaternary Structure Modeling Through Chemical Cross-Linking Mass Spectrometry: Extending TX-MS Jupyter Reports. Journal of Visualized Experiments : Jove. PMID 34747410 DOI: 10.3791/60311 |
0.309 |
|
| 2020 |
Khakzad H, Happonen L, Tran Van Nhieu G, Malmström J, Malmström L. Cross-Linking MS of the Complement System MAC Assembled on Live Gram-Positive Bacteria. Frontiers in Genetics. 11: 612475. PMID 33488677 DOI: 10.3389/fgene.2020.612475 |
0.328 |
|
| 2020 |
Röst HL, Rosenberger G, Navarro P, Gillet L, Miladinović SM, Schubert OT, Wolski W, Collins BC, Malmström J, Malmström L, Aebersold R. Publisher Correction: OpenSWATH enables automated, targeted analysis of data-independent acquisition MS data. Nature Biotechnology. PMID 32094660 DOI: 10.1038/S41587-020-0457-8 |
0.303 |
|
| 2020 |
Chowdhury S, Happonen L, Khakzad H, Malmström L, Malmström J. Structural proteomics, electron cryo-microscopy and structural modeling approaches in bacteria-human protein interactions. Medical Microbiology and Immunology. PMID 32072248 DOI: 10.1007/S00430-020-00663-5 |
0.39 |
|
| 2019 |
Happonen L, Hauri S, Svensson Birkedal G, Karlsson C, de Neergaard T, Khakzad H, Nordenfelt P, Wikström M, Wisniewska M, Björck L, Malmström L, Malmström J. A quantitative Streptococcus pyogenes-human protein-protein interaction map reveals localization of opsonizing antibodies. Nature Communications. 10: 2727. PMID 31227708 DOI: 10.1038/S41467-019-10583-5 |
0.385 |
|
| 2019 |
Khakzad H, Malmström J, Malmström L. Greedy de novo motif discovery to construct motif repositories for bacterial proteomes. Bmc Bioinformatics. 20: 141. PMID 30999854 DOI: 10.1186/S12859-019-2686-8 |
0.444 |
|
| 2019 |
Malmström L. Computational Proteomics with Jupyter and Python. Methods in Molecular Biology (Clifton, N.J.). 1977: 237-248. PMID 30980332 DOI: 10.1007/978-1-4939-9232-4_15 |
0.336 |
|
| 2019 |
Hauri S, Khakzad H, Happonen L, Teleman J, Malmström J, Malmström L. Rapid determination of quaternary protein structures in complex biological samples. Nature Communications. 10: 192. PMID 30643114 DOI: 10.1038/S41467-018-07986-1 |
0.456 |
|
| 2018 |
Leslie Pedrioli DM, Leutert M, Bilan V, Nowak K, Gunasekera K, Ferrari E, Imhof R, Malmström L, Hottiger MO. Comprehensive ADP-ribosylome analysis identifies tyrosine as an ADP-ribose acceptor site. Embo Reports. PMID 29954836 DOI: 10.15252/Embr.201745310 |
0.334 |
|
| 2018 |
Åhrman E, Hallgren O, Malmström L, Hedström U, Malmström A, Bjermer L, Zhou XH, Westergren-Thorsson G, Malmström J. Quantitative proteomic characterization of the lung extracellular matrix in chronic obstructive pulmonary disease and idiopathic pulmonary fibrosis. Journal of Proteomics. PMID 29501846 DOI: 10.1016/J.Jprot.2018.02.027 |
0.319 |
|
| 2017 |
Rosenberger G, Liu Y, Röst HL, Ludwig C, Buil A, Bensimon A, Soste M, Spector TD, Dermitzakis ET, Collins BC, Malmström L, Aebersold R. Inference and quantification of peptidoforms in large sample cohorts by SWATH-MS. Nature Biotechnology. PMID 28604659 DOI: 10.1038/Nbt.3908 |
0.378 |
|
| 2017 |
Sjöholm K, Kilsgård O, Teleman J, Happonen L, Malmström L, Malmström J. Targeted Proteomics and Absolute Protein Quantification for the Construction of a Stoichiometric Host-Pathogen Surface Density Model. Molecular & Cellular Proteomics : McP. 16: S29-S41. PMID 28183813 DOI: 10.1074/Mcp.M116.063966 |
0.419 |
|
| 2016 |
Röst HL, Sachsenberg T, Aiche S, Bielow C, Weisser H, Aicheler F, Andreotti S, Ehrlich HC, Gutenbrunner P, Kenar E, Liang X, Nahnsen S, Nilse L, Pfeuffer J, Rosenberger G, et al. OpenMS: a flexible open-source software platform for mass spectrometry data analysis. Nature Methods. 13: 741-748. PMID 27575624 DOI: 10.1038/Nmeth.3959 |
0.356 |
|
| 2016 |
Röst HL, Liu Y, D'Agostino G, Zanella M, Navarro P, Rosenberger G, Collins BC, Gillet L, Testa G, Malmström L, Aebersold R. TRIC: an automated alignment strategy for reproducible protein quantification in targeted proteomics. Nature Methods. PMID 27479329 DOI: 10.1038/Nmeth.3954 |
0.375 |
|
| 2016 |
Malmström E, Kilsgård O, Hauri S, Smeds E, Herwald H, Malmström L, Malmström J. Large-scale inference of protein tissue origin in gram-positive sepsis plasma using quantitative targeted proteomics. Nature Communications. 7: 10261. PMID 26732734 DOI: 10.1038/Ncomms10261 |
0.393 |
|
| 2015 |
Röst HL, Malmström L, Aebersold R. Reproducible quantitative proteotype data matrices for systems biology. Molecular Biology of the Cell. 26: 3926-31. PMID 26543201 DOI: 10.1091/Mbc.E15-07-0507 |
0.422 |
|
| 2015 |
Walzthoeni T, Joachimiak LA, Rosenberger G, Röst HL, Malmström L, Leitner A, Frydman J, Aebersold R. xTract: software for characterizing conformational changes of protein complexes by quantitative cross-linking mass spectrometry. Nature Methods. PMID 26501516 DOI: 10.1038/Nmeth.3631 |
0.401 |
|
| 2015 |
Malmström L, Bakochi A, Svensson G, Kilsgård O, Lantz H, Petersson AC, Hauri S, Karlsson C, Malmström J. Quantitative proteogenomics of human pathogens using DIA-MS. Journal of Proteomics. 129: 98-107. PMID 26381203 DOI: 10.1016/J.Jprot.2015.09.012 |
0.399 |
|
| 2015 |
Parker SJ, Rost H, Rosenberger G, Collins BC, Malmström L, Amodei D, Venkatraman V, Raedschelders K, Van Eyk JE, Aebersold R. Identification of a Set of Conserved Eukaryotic Internal Retention Time Standards for Data-independent Acquisition Mass Spectrometry. Molecular & Cellular Proteomics : McP. 14: 2800-13. PMID 26199342 DOI: 10.1074/Mcp.O114.042267 |
0.326 |
|
| 2015 |
Sjöström M, Ossola R, Breslin T, Rinner O, Malmström L, Schmidt A, Aebersold R, Malmström J, Niméus E. A Combined Shotgun and Targeted Mass Spectrometry Strategy for Breast Cancer Biomarker Discovery. Journal of Proteome Research. PMID 25944384 DOI: 10.1021/Acs.Jproteome.5B00315 |
0.391 |
|
| 2015 |
Röst HL, Schmitt U, Aebersold R, Malmström L. Fast and Efficient XML Data Access for Next-Generation Mass Spectrometry. Plos One. 10: e0125108. PMID 25927999 DOI: 10.1371/Journal.Pone.0125108 |
0.346 |
|
| 2015 |
Röst HL, Rosenberger G, Aebersold R, Malmström L. Efficient visualization of high-throughput targeted proteomics experiments: TAPIR. Bioinformatics (Oxford, England). 31: 2415-7. PMID 25788625 DOI: 10.1093/Bioinformatics/Btv152 |
0.366 |
|
| 2015 |
Teleman J, Röst HL, Rosenberger G, Schmitt U, Malmström L, Malmström J, Levander F. DIANA--algorithmic improvements for analysis of data-independent acquisition MS data. Bioinformatics (Oxford, England). 31: 555-62. PMID 25348213 DOI: 10.1093/Bioinformatics/Btu686 |
0.345 |
|
| 2014 |
Wisniewska M, Happonen L, Kahn F, Varjosalo M, Malmström L, Rosenberger G, Karlsson C, Cazzamali G, Pozdnyakova I, Frick IM, Björck L, Streicher W, Malmström J, Wikström M. Functional and structural properties of a novel protein and virulence factor (Protein sHIP) in Streptococcus pyogenes. The Journal of Biological Chemistry. 289: 18175-88. PMID 24825900 DOI: 10.1074/Jbc.M114.565978 |
0.418 |
|
| 2014 |
Teleman J, Dowsey AW, Gonzalez-Galarza FF, Perkins S, Pratt B, Röst HL, Malmström L, Malmström J, Jones AR, Deutsch EW, Levander F. Numerical compression schemes for proteomics mass spectrometry data. Molecular & Cellular Proteomics : McP. 13: 1537-42. PMID 24677029 DOI: 10.1074/Mcp.O114.037879 |
0.329 |
|
| 2014 |
Thaipisuttikul I, Hittle LE, Chandra R, Zangari D, Dixon CL, Garrett TA, Rasko DA, Dasgupta N, Moskowitz SM, Malmström L, Goodlett DR, Miller SI, Bishop RE, Ernst RK. A divergent Pseudomonas aeruginosa palmitoyltransferase essential for cystic fibrosis-specific lipid A. Molecular Microbiology. 91: 158-74. PMID 24283944 DOI: 10.1111/Mmi.12451 |
0.488 |
|
| 2014 |
Kalliomäki M, Kouvonen P, Koh C, Collins B, Malmström L, Aebersold R. P-003: Detection of bacterial and host proteins from a single colonic biopsy sample by a new mass spectrometry-based assay in pediatric ulcerative colitis Journal of Crohn's and Colitis. 8: S395. DOI: 10.1016/S1873-9946(14)50007-4 |
0.312 |
|
| 2014 |
Quandt A, Espona L, Balasko A, Weisser H, Brusniak MY, Kunszt P, Aebersold R, Malmström L. Using synthetic peptides to benchmark peptide identification software and search parameters for MS/MS data analysis Eupa Open Proteomics. 5: 21-31. DOI: 10.1016/J.Euprot.2014.10.001 |
0.324 |
|
| 2012 |
Reker D, Malmström L. Bioinformatic challenges in targeted proteomics. Journal of Proteome Research. 11: 4393-402. PMID 22866949 DOI: 10.1021/Pr300276F |
0.341 |
|
| 2011 |
Drew K, Winters P, Butterfoss GL, Berstis V, Uplinger K, Armstrong J, Riffle M, Schweighofer E, Bovermann B, Goodlett DR, Davis TN, Shasha D, Malmström L, Bonneau R. The Proteome Folding Project: proteome-scale prediction of structure and function. Genome Research. 21: 1981-94. PMID 21824995 DOI: 10.1101/Gr.121475.111 |
0.555 |
|
| 2010 |
Malmström L, Goodlett DR. Protein structure modeling. Methods in Molecular Biology (Clifton, N.J.). 673: 63-72. PMID 20835793 DOI: 10.1007/978-1-60761-842-3_5 |
0.574 |
|
| 2010 |
Nunn BL, Ting YS, Malmström L, Tsai YS, Squier A, Goodlett DR, Harvey HR. The path to preservation: Using proteomics to decipher the fate of diatom proteins during microbial degradation Limnology and Oceanography. 55: 1790-1804. DOI: 10.4319/Lo.2010.55.4.1790 |
0.712 |
|
| 2009 |
Kalantari F, Auguste P, Ziafazeli T, Tzimas G, Malmström L, Bioulac-Sage P, Boismenu D, Vali H, Chevet E. Proteomics analysis of liver pathological calcification suggests a role for the IQ motif containing GTPase activating protein 1 in myofibroblast function. Proteomics. Clinical Applications. 3: 307-21. PMID 26238749 DOI: 10.1002/Prca.200780133 |
0.339 |
|
| 2009 |
Nunn BL, Aker JR, Shaffer SA, Tsai S, Strzepek RF, Boyd PW, Freeman TL, Brittnacher M, Malmström L, Goodlett DR. Deciphering diatom biochemical pathways via whole-cell proteomics. Aquatic Microbial Ecology : International Journal. 55: 241-253. PMID 19829762 DOI: 10.3354/Ame01284 |
0.698 |
|
| 2009 |
Pacheco B, Maccarana M, Goodlett DR, Malmström A, Malmström L. Identification of the active site of DS-epimerase 1 and requirement of N-glycosylation for enzyme function. The Journal of Biological Chemistry. 284: 1741-7. PMID 19004833 DOI: 10.1074/Jbc.M805479200 |
0.492 |
|
| 2009 |
Goo YA, Liu AY, Ryu S, Shaffer SA, Malmström L, Page L, Nguyen LT, Doneanu CE, Goodlett DR. Identification of secreted glycoproteins of human prostate and bladder stromal cells by comparative quantitative proteomics. The Prostate. 69: 49-61. PMID 18792917 DOI: 10.1002/Pros.20853 |
0.651 |
|
| 2007 |
Das R, Qian B, Raman S, Vernon R, Thompson J, Bradley P, Khare S, Tyka MD, Bhat D, Chivian D, Kim DE, Sheffler WH, Malmström L, Wollacott AM, Wang C, et al. Structure prediction for CASP7 targets using extensive all-atom refinement with Rosetta@home. Proteins. 69: 118-28. PMID 17894356 DOI: 10.1002/Prot.21636 |
0.331 |
|
| 2007 |
Malmström L, Riffle M, Strauss CEM, Chivian D, Davis TN, Bonneau R, Baker D. Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology Plos Biology. 5. PMID 17373854 DOI: 10.1371/Journal.Pbio.0050076 |
0.406 |
|
| 2007 |
Malmström E, Sennström M, Holmberg A, Frielingsdorf H, Eklund E, Malmström L, Tufvesson E, Gomez MF, Westergren-Thorsson G, Ekman-Ordeberg G, Malmström A. The importance of fibroblasts in remodelling of the human uterine cervix during pregnancy and parturition. Molecular Human Reproduction. 13: 333-41. PMID 17337476 DOI: 10.1093/Molehr/Gal117 |
0.31 |
|
| 2006 |
Malmström L, Marko-Varga G, Westergren-Thorsson G, Laurell T, Malmström J. 2DDB - a bioinformatics solution for analysis of quantitative proteomics data. Bmc Bioinformatics. 7: 158. PMID 16549013 DOI: 10.1186/1471-2105-7-158 |
0.312 |
|
| 2005 |
Kim DE, Chivian D, Malmström L, Baker D. Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins. 61: 193-200. PMID 16187362 DOI: 10.1002/Prot.20737 |
0.325 |
|
| 2005 |
Chivian D, Kim DE, Malmström L, Schonbrun J, Rohl CA, Baker D. Prediction of CASP6 structures using automated Robetta protocols. Proteins. 61: 157-66. PMID 16187358 DOI: 10.1002/Prot.20733 |
0.331 |
|
| 2005 |
Bradley P, Malmström L, Qian B, Schonbrun J, Chivian D, Kim DE, Meiler J, Misura KM, Baker D. Free modeling with Rosetta in CASP6. Proteins. 61: 128-34. PMID 16187354 DOI: 10.1002/Prot.20729 |
0.39 |
|
| 2005 |
Riffle M, Malmström L, Davis TN. The Yeast Resource Center Public Data Repository Nucleic Acids Research. 33. PMID 15608220 DOI: 10.1093/Nar/Gki073 |
0.392 |
|
| 2005 |
Malmström J, Malmström L, Marko-Varga G. Proteomics: A new research area for the biomedical field Journal of Organ Dysfunction. 1: 83-94. DOI: 10.1080/17471060500223910 |
0.313 |
|
| 2004 |
Malmström J, Larsen K, Malmström L, Tufvesson E, Parker K, Marchese J, Williamson B, Hattan S, Patterson D, Martin S, Graber A, Juhasz HP, Westergren-Thorsson G, Marko-Varga G. Proteome annotations and identifications of the human pulmonary fibroblast. Journal of Proteome Research. 3: 525-37. PMID 15253434 DOI: 10.1021/Pr034104V |
0.444 |
|
| 2003 |
Hazbun TR, Malmström L, Anderson S, Graczyk BJ, Fox B, Riffle M, Sundin BA, Aranda JD, McDonald WH, Chiu CH, Snydsman BE, Bradley P, Muller EG, Fields S, Baker D, et al. Assigning function to yeast proteins by integration of technologies. Molecular Cell. 12: 1353-65. PMID 14690591 DOI: 10.1016/S1097-2765(03)00476-3 |
0.464 |
|
| 2003 |
Malmström J, Larsen K, Malmström L, Tufvesson E, Parker K, Marchese J, Williamson B, Patterson D, Martin S, Juhasz P, Westergren-Thorsson G, Marko-Varga G. Nanocapillary liquid chromatography interfaced to tandem matrix-assisted laser desorption/ionization and electrospray ionization-mass spectrometry: mapping the nuclear proteome of human fibroblasts. Electrophoresis. 24: 3806-14. PMID 14613209 DOI: 10.1002/Elps.200305619 |
0.432 |
|
| 2003 |
Chivian D, Kim DE, Malmström L, Bradley P, Robertson T, Murphy P, Strauss CE, Bonneau R, Rohl CA, Baker D. Automated prediction of CASP-5 structures using the Robetta server. Proteins. 53: 524-33. PMID 14579342 DOI: 10.1002/Prot.10529 |
0.326 |
|
| 2002 |
Malmström L, Malmström J, Marko-Varga G, Westergren-Thorsson G. Proteomic 2DE database for spot selection, automated annotation, and data analysis. Journal of Proteome Research. 1: 135-8. PMID 12643533 DOI: 10.1021/Pr010004I |
0.351 |
|
| 2002 |
Bonneau R, Strauss CE, Rohl CA, Chivian D, Bradley P, Malmström L, Robertson T, Baker D. De novo prediction of three-dimensional structures for major protein families. Journal of Molecular Biology. 322: 65-78. PMID 12215415 DOI: 10.1016/S0022-2836(02)00698-8 |
0.42 |
|
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